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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ), 'gf_id' => 'HOM05D001175', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001175' ), 'data_identifier' => 'HOM05D001175', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001175', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16790' => 'bna', 'A02p41940' => 'bna', 'A03p56060' => 'bna', 'A05p21800' => 'bna', 'A08p21100' => 'bna', 'A10p07740' => 'bna', 'Aa31LG3G19140' => 'aar', 'Aa31LG9G14130' => 'aar', 'Aa31LG9G14150' => 'aar', 'Aa31sc383G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4589' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1155' => 'aag', 'Actinidia03105' => 'ach', 'Actinidia03106' => 'ach', 'Actinidia03443' => 'ach', 'Actinidia05227' => 'ach', 'Actinidia15168' => 'ach', 'Actinidia16587' => 'ach', 'Actinidia27407' => 'ach', 'Actinidia29510' => 'ach', 'Actinidia31806' => 'ach', 'Actinidia32892' => 'ach', 'Actinidia34083' => 'ach', 'Ah.05g169310' => 'amhyb', 'Ah.07g209000' => 'amhyb', 'Ah.13g068280' => 'amhyb', 'Ah.16g105170' => 'amhyb', 'AL1G51990' => 'aly', 'AL7G27570' => 'aly', 'AL7G27580' => 'aly', 'AL8G38870' => 'aly', 'Aqoxy5G02236' => 'aox', 'Aqoxy7G00439' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2FQ9M1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2JVF5K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3THH2M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8WX4TX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ5K6I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI3IXZ' => 'arhy', 'AT1G43850' => 'ath', 'AT4G25515' => 'ath', 'AT4G25520' => 'ath', 'AT5G62090' => 'ath', 'ATR0757G064' => 'atr', 'ATR1136G212' => 'atr', 'Atru.chr1.514' => 'acertr', 'Atru.chr13.1668' => 'acertr', 'AUR62010649' => 'cqu', 'AUR62013477' => 'cqu', 'AUR62013478' => 'cqu', 'AUR62016027' => 'cqu', 'AUR62017290' => 'cqu', 'AUR62021232' => 'cqu', 'AUR62026794' => 'cqu', 'BcaB02g09622' => 'bca', 'BcaB02g09623' => 'bca', 'BcaB02g11415' => 'bca', 'BcaB03g12475' => 'bca', 'BcaB04g17755' => 'bca', 'BcaB07g29802' => 'bca', 'BcaB07g33973' => 'bca', 'BcaC03g18119' => 'bca', 'BcaC05g27658' => 'bca', 'BcaC06g32804' => 'bca', 'BcaC06g32805' => 'bca', 'BcaC06g32806' => 'bca', 'BcaC06g32807' => 'bca', 'BcaC07g38198' => 'bca', 'BcaC08g42823' => 'bca', 'BcaC09g50765' => 'bca', 'BcaNung01412' => 'bca', 'BcaNung01413' => 'bca', 'BcaNung03698' => 'bca', 'BolC1t02031H' => 'bol', 'BolC2t12242H' => 'bol', 'BolC3t18748H' => 'bol', 'BolC3t18749H' => 'bol', 'BolC5t32378H' => 'bol', 'BolC6t35168H' => 'bol', 'BolC7t45922H' => 'bol', 'BolC7t45923H' => 'bol', 'BolC8t48622H' => 'bol', 'BraA01t01632Z' => 'bra', 'BraA02t09129Z' => 'bra', 'BraA03t14675Z' => 'bra', 'BraA03t14676Z' => 'bra', 'BraA05t21101Z' => 'bra', 'BraA08t34060Z' => 'bra', 'BraSC36t46031Z' => 'bra', 'C01p21070' => 'bna', 'C02p61850' => 'bna', 'C03p64870' => 'bna', 'C05p36460' => 'bna', 'C06p00370' => 'bna', 'C06p00400' => 'bna', 'C07p54380' => 'bna', 'C08p09540' => 'bna', 'CAN.G1154.1' => 'can', 'CAN.G1154.2' => 'can', 'CAN.G1154.3' => 'can', 'CAN.G319.4' => 'can', 'CAN.G516.8' => 'can', 'CAN.G548.1' => 'can', 'CAN.G657.1' => 'can', 'CANSAT21G1123' => 'cansat', 'CANSAT21G1763' => 'cansat', 'CANSAT25G2918' => 'cansat', 'CARHR035410' => 'chi', 'CARHR232920' => 'chi', 'CARHR232930' => 'chi', 'CARHR275880' => 'chi', 'Carub.0001s3479' => 'cru', 'Carub.0007s1547' => 'cru', 'Carub.0007s1548' => 'cru', 'Carub.0008s2277' => 'cru', 'Ca_07216_v3' => 'car', 'Ca_16645_v3' => 'car', 'CBR_g19452' => 'cbr', 'CBR_g66706' => 'cbr', 'Cc02_g03380' => 'ccan', 'Cc07_g18430' => 'ccan', 'Cc08_g14030' => 'ccan', 'Cc10_g13110' => 'ccan', 'CDE02G0513' => 'cde', 'CDE02G1305' => 'cde', 'CDE02G2192' => 'cde', 'CDE06G0884' => 'cde', 'CDE06G0923' => 'cde', 'CDE08G0080' => 'cde', 'CDE08G0965' => 'cde', 'CDE08G1383' => 'cde', 'CDE11G0657' => 'cde', 'CDE11G0996' => 'cde', 'Cfa008283' => 'cfa', 'Cfa012107' => 'cfa', 'Cfa018381' => 'cfa', 'Ciclev10000185m.g' => 'ccl', 'Ciclev10004290m.g' => 'ccl', 'Ciclev10019047m.g' => 'ccl', 'CiPaw.03G102800' => 'cil', 'CiPaw.04G067200' => 'cil', 'CiPaw.11G140900' => 'cil', 'CiPaw.15G022600' => 'cil', 'CiPaw.16G018500' => 'cil', 'ClCG01G005640' => 'cla', 'ClCG05G007850' => 'cla', 'ClCG08G002750' => 'cla', 'ClCG08G006370' => 'cla', 'COL.COLO4_14267' => 'col', 'COL.COLO4_33802' => 'col', 'COL.COLO4_35731' => 'col', 'Cpa.g.sc107.10' => 'cpa', 'Cpa.g.sc26.90' => 'cpa', 'Cpa.g.sc42.150' => 'cpa', 'CsaV3_3G016850' => 'csa', 'CsaV3_5G005860' => 'csa', 'CsaV3_6G031050' => 'csa', 'CsaV3_6G035610' => 'csa', 'CSS0003475' => 'camsi', 'CSS0007687' => 'camsi', 'CSS0010406' => 'camsi', 'CSS0031578' => 'camsi', 'CSS0039656' => 'camsi', 'DCAR_001115' => 'dca', 'DCAR_001215' => 'dca', 'DCAR_001342' => 'dca', 'DCAR_003229' => 'dca', 'DCAR_008874' => 'dca', 'DCAR_010237' => 'dca', 'DCAR_018172' => 'dca', 'DCAR_020234' => 'dca', 'Dinv07378' => 'din', 'Dinv25795' => 'din', 'Dinv28476' => 'din', 'Dinv35181' => 'din', 'Dinv37690' => 'din', 'Dinv41135' => 'din', 'Duzib041G0421' => 'dzi', 'Duzib068G0321' => 'dzi', 'Duzib084G1294' => 'dzi', 'Duzib093G0267' => 'dzi', 'Duzib116G0064' => 'dzi', 'Duzib147G0828' => 'dzi', 'Duzib187G0054' => 'dzi', 'Duzib205G0391' => 'dzi', 'Duzib264G0298' => 'dzi', 'ECA232G0133' => 'eca', 'ECA232G3725' => 'eca', 'ECA233G1946' => 'eca', 'ECA238G4782' => 'eca', 'ECA247G1079' => 'eca', 'EL10Ac1g01447' => 'bvu', 'EL10Ac1g02183' => 'bvu', 'EL10Ac3g05698' => 'bvu', 'EL10Ac5g12730' => 'bvu', 'EL10Ac5g12731' => 'bvu', 'EL10Ac6g13980' => 'bvu', 'EL10Ac7g17948' => 'bvu', 'EL10Ac9g21540' => 'bvu', 'EL10As19g24199' => 'bvu', 'EL10As3g23325' => 'bvu', 'EL10As3g23326' => 'bvu', 'Eucgr.F02753' => 'egr', 'Eucgr.F04275' => 'egr', 'Eucgr.K00227' => 'egr', 'FAN01G2900' => 'fan', 'FAN03G1081' => 'fan', 'FAN03G2528' => 'fan', 'FAN04G1453' => 'fan', 'FAN04G1921' => 'fan', 'FAN06G4630' => 'fan', 'FAN06G4862' => 'fan', 'FAN08G3135' => 'fan', 'FAN09G1163' => 'fan', 'FAN10G1646' => 'fan', 'FAN10G3339' => 'fan', 'FAN13G2259' => 'fan', 'FAN14G4699' => 'fan', 'FAN15G1627' => 'fan', 'FAN18G1412' => 'fan', 'FAN20G0732' => 'fan', 'FAN24G2465' => 'fan', 'FAN25G2825' => 'fan', 'FAN27G0104' => 'fan', 'FvH4_2g14890' => 'fve', 'FvH4_5g01530' => 'fve', 'FvH4_7g29060' => 'fve', 'Glyma.04G241900' => 'gma', 'Glyma.06G121500' => 'gma', 'Glyma.09G146000' => 'gma', 'Glyma.09G146200' => 'gma', 'Glyma.13G037600' => 'gma', 'Glyma.14G119800' => 'gma', 'Glyma.16G198200' => 'gma', 'Glyma.16G198300' => 'gma', 'Gohir.A02G067800' => 'ghi', 'Gohir.A02G126000' => 'ghi', 'Gohir.A08G082600' => 'ghi', 'Gohir.A09G040200' => 'ghi', 'Gohir.A11G009600' => 'ghi', 'Gohir.A11G057000' => 'ghi', 'Gohir.A12G260400' => 'ghi', 'Gohir.D02G073800' => 'ghi', 'Gohir.D03G061702' => 'ghi', 'Gohir.D08G113000' => 'ghi', 'Gohir.D09G041000' => 'ghi', 'Gohir.D11G008900' => 'ghi', 'Gohir.D11G061100' => 'ghi', 'Gohir.D12G261200' => 'ghi', 'Gorai.004G121400' => 'gra', 'Gorai.005G083200' => 'gra', 'Gorai.006G046800' => 'gra', 'Gorai.007G010500' => 'gra', 'Gorai.007G065800' => 'gra', 'Gorai.008G280000' => 'gra', 'Gorai.013G106300' => 'gra', 'GSVIVG01010013001' => 'vvi', 'GSVIVG01010616001' => 'vvi', 'GSVIVG01019855001' => 'vvi', 'GSVIVG01026491001' => 'vvi', 'HanXRQChr04g0109511' => 'han', 'HanXRQChr05g0141281' => 'han', 'HanXRQChr13g0393171' => 'han', 'HanXRQChr13g0417891' => 'han', 'HanXRQChr14g0462081' => 'han', 'HanXRQChr15g0484631' => 'han', 'Haze_08944' => 'cav', 'Haze_13752' => 'cav', 'Haze_17691' => 'cav', 'Haze_20476' => 'cav', 'Haze_25225' => 'cav', 'Hma1.2p1_0099F.1_g048540' => 'hma', 'Hma1.2p1_0270F.1_g108410' => 'hma', 'Hma1.2p1_0655F.1_g196730' => 'hma', 'HPP92_002047' => 'vpl', 'HPP92_003271' => 'vpl', 'Hund11527' => 'sun', 'Hund11771' => 'sun', 'Hund17389' => 'sun', 'Hund26736' => 'sun', 'Lalb_Chr01g0013671' => 'lal', 'Lalb_Chr01g0013681' => 'lal', 'Lalb_Chr08g0240841' => 'lal', 'Lalb_Chr11g0066371' => 'lal', 'Lalb_Chr19g0131031' => 'lal', 'Lalb_Chr19g0131041' => 'lal', 'Lalb_Chr19g0131051' => 'lal', 'Lalb_Chr23g0271321' => 'lal', 'Lj1A993T68' => 'lonja', 'Lj1g0005719' => 'lja', 'Lj1g0024089' => 'lja', 'Lj2g0010509' => 'lja', 'Lj4A690T48' => 'lonja', 'Lj6C341T0' => 'lonja', 'Lj7C362G7' => 'lonja', 'Lj8A28G36' => 'lonja', 'Lj9A220T25' => 'lonja', 'LjContig00238g0002815' => 'lja', 'Lsat_1_v5_gn_1_9801' => 'lsa', 'Lsat_1_v5_gn_2_133101' => 'lsa', 'Lsat_1_v5_gn_8_7441' => 'lsa', 'Lsat_1_v5_gn_9_54401' => 'lsa', 'Manes.02G173700' => 'mes', 'Manes.06G144100' => 'mes', 'Manes.13G083700' => 'mes', 'Manes.14G028800' => 'mes', 'Manes.18G086300' => 'mes', 'Mapoly0005s0280' => 'mpo', 'Mapoly0030s0035' => 'mpo', 'MBI03_g35247_MAGBIO' => 'mbi', 'MBI04_g02074_MAGBIO' => 'mbi', 'MBI06_g29670_MAGBIO' => 'mbi', 'MBI18_g34077_MAGBIO' => 'mbi', 'MD01G1197300' => 'mdo', 'MD02G1101700' => 'mdo', 'MD05G1012000' => 'mdo', 'MD07G1264600' => 'mdo', 'MD07G1264700' => 'mdo', 'MD10G1012000' => 'mdo', 'Medtr1g029400' => 'mtr', 'Medtr3g089075' => 'mtr', 'MELO3C005370.2' => 'cme', 'MELO3C006880.2' => 'cme', 'MELO3C008420.2' => 'cme', 'MELO3C010585.2' => 'cme', 'Migut.A00925' => 'egut', 'Migut.B01694' => 'egut', 'Migut.C01103' => 'egut', 'Migut.F00373' => 'egut', 'Migut.F01143' => 'egut', 'Migut.H00725' => 'egut', 'Migut.N03246' => 'egut', 'MSTRG.107' => 'ama', 'MSTRG.1381' => 'ama', 'MSTRG.22386' => 'ama', 'MSTRG.24183' => 'ama', 'MSTRG.25337' => 'ama', 'MSTRG.8440' => 'ama', 'MSTRG.8441' => 'ama', 'MSTRG.8761' => 'ama', 'Nitab4.5_0000174g0220' => 'nta', 'Nitab4.5_0000856g0050' => 'nta', 'Nitab4.5_0001083g0090' => 'nta', 'Nitab4.5_0001559g0070' => 'nta', 'Nitab4.5_0002972g0010' => 'nta', 'Nitab4.5_0003517g0030' => 'nta', 'Nitab4.5_0004560g0050' => 'nta', 'Nitab4.5_0010049g0020' => 'nta', 'Nn1g01368' => 'nnu', 'Nn1g06258' => 'nnu', 'Nn5g28571' => 'nnu', 'Nn6g34243' => 'nnu', 'Oeu001557.1' => 'oeu', 'Oeu002393.1' => 'oeu', 'Oeu004132.1' => 'oeu', 'Oeu004133.1' => 'oeu', 'Oeu021765.1' => 'oeu', 'Oeu022551.1' => 'oeu', 'Oeu025717.1' => 'oeu', 'Oeu030123.1' => 'oeu', 'Oeu031056.1' => 'oeu', 'Oeu045996.1' => 'oeu', 'Oeu045997.1' => 'oeu', 'Oeu062363.1' => 'oeu', 'Oeu062774.3' => 'oeu', 'Oeu064164.1' => 'oeu', 'Os06g0126000' => 'osa', 'Os11g0207000' => 'osa', 'Os11g0207100' => 'osa', 'Peaxi162Scf00033g00415' => 'pax', 'Peaxi162Scf00066g02017' => 'pax', 'Peaxi162Scf00183g00037' => 'pax', 'Peaxi162Scf00915g00255' => 'pax', 'PGR042G1127' => 'pgr', 'PGR044G1174' => 'pgr', 'PGR142G0206' => 'pgr', 'PGSC0003DMG400014269' => 'stu', 'PGSC0003DMG400041650' => 'stu', 'Phvul.001G064200' => 'pvu', 'Phvul.004G121300' => 'pvu', 'Phvul.004G121400' => 'pvu', 'Phvul.009G134000' => 'pvu', 'Potri.001G109901' => 'ptr', 'Potri.001G355900' => 'ptr', 'Potri.002G072900' => 'ptr', 'Potri.003G121800' => 'ptr', 'Potri.005G058501' => 'ptr', 'Potri.005G186900' => 'ptr', 'Potri.007G109400' => 'ptr', 'Potri.010G052150' => 'ptr', 'Potri.012G136100' => 'ptr', 'Potri.013G089900' => 'ptr', 'Potri.015G138500' => 'ptr', 'Pp3c16_15040' => 'ppa', 'Pp3c16_1720' => 'ppa', 'Pp3c16_1979' => 'ppa', 'Pp3c16_1990' => 'ppa', 'Pp3c25_7790' => 'ppa', 'Pp3c25_7810' => 'ppa', 'Pp3c25_7930' => 'ppa', 'Pp3c25_7960' => 'ppa', 'Pp3c4_30018' => 'ppa', 'Pp3c5_5980' => 'ppa', 'Pp3c6_27010' => 'ppa', 'Prupe.2G290500' => 'ppe', 'Prupe.5G091500' => 'ppe', 'Prupe.8G017000' => 'ppe', 'Psat0s5292g0040' => 'psa', 'Psat1g107280' => 'psa', 'Psat5g028400' => 'psa', 'Psat5g081560' => 'psa', 'Psat6g039480' => 'psa', 'Psat6g134640' => 'psa', 'Psat7g060560' => 'psa', 'PSO017G4885' => 'pso', 'PSO170G0978' => 'pso', 'PSO478G1523' => 'pso', 'PSO541G4630' => 'pso', 'PSO675G1006' => 'pso', 'PSO782G4201' => 'pso', 'QL02p091955' => 'qlo', 'QL06p028692' => 'qlo', 'QL09p014926' => 'qlo', 'QL09p029009' => 'qlo', 'QL12p017323' => 'qlo', 'RcHm_v2.0_Chr1g0376781' => 'rch', 'RcHm_v2.0_Chr6g0277461' => 'rch', 'RcHm_v2.0_Chr7g0199161' => 'rch', 'Rhsim01G0180400' => 'rsi', 'Rhsim04G0183200' => 'rsi', 'Rhsim07G0094500' => 'rsi', 'Rhsim09G0196500' => 'rsi', 'Rhsim10G0135400' => 'rsi', 'Rhsim11G0077100' => 'rsi', 'Sabra02G0057300' => 'sbr', 'Sabra05G0050300' => 'sbr', 'Sabra05G0142800' => 'sbr', 'Sabra07G0089500' => 'sbr', 'Sabra12G0102300' => 'sbr', 'Sabra15G0149600' => 'sbr', 'SalBow2G1271' => 'sbo', 'SalBow4G1481' => 'sbo', 'SalBow6G3246' => 'sbo', 'SalBow6G4047' => 'sbo', 'Sc02g0004490' => 'sci', 'Sc13g0008450' => 'sci', 'Sc19g0001690' => 'sci', 'Sed0002353' => 'sed', 'Sed0008095' => 'sed', 'Sed0008940' => 'sed', 'Sed0013770' => 'sed', 'Sed0020201' => 'sed', 'Sed0021141' => 'sed', 'Sed0026488' => 'sed', 'SEGI_10917' => 'sgi', 'SEGI_34871' => 'sgi', 'SGA_v2.0_scaffold10G05381' => 'sas', 'SGA_v2.0_scaffold19G08630' => 'sas', 'SGA_v2.0_scaffold221G42723' => 'sas', 'SGA_v2.0_scaffold221G42725' => 'sas', 'SGA_v2.0_scaffold25G11150' => 'sas', 'SGA_v2.0_scaffold90G27752' => 'sas', 'SHI09276' => 'shi', 'SMO118G0058' => 'smo', 'SMO358G0185' => 'smo', 'SMO367G0643' => 'smo', 'Solyc03g026190.3' => 'sly', 'Solyc06g059750.3' => 'sly', 'Solyc06g059760.3' => 'sly', 'Solyc11g005990.2' => 'sly', 'Sopen03g005060' => 'spe', 'Sopen06g019820' => 'spe', 'Sopen06g019830' => 'spe', 'Sopen11g001930' => 'spe', 'Sp1g33070' => 'spa', 'Sp2g25260' => 'spa', 'Sp7g23530' => 'spa', 'Sp7g23540' => 'spa', 'TAR374G0953' => 'tar', 'TAR375G0292' => 'tar', 'TAR375G0307' => 'tar', 'TAR381G1233' => 'tar', 'TAR625G1326' => 'tar', 'TAR628G0144' => 'tar', 'TAR629G1730' => 'tar', 'TAR636G2633' => 'tar', 'THA.LOC104798857' => 'tha', 'THA.LOC104798863' => 'tha', 'THA.LOC104800262' => 'tha', 'THA.LOC104812066' => 'tha', 'THA.LOC104818274' => 'tha', 'Thecc.01G131100' => 'tca', 'Thecc.03G171000' => 'tca', 'Thecc.03G271800' => 'tca', 'Thecc.08G142300' => 'tca', 'Thhalv10003661m.g' => 'esa', 'Thhalv10011234m.g' => 'esa', 'Thhalv10012891m.g' => 'esa', 'Thhalv10012897m.g' => 'esa', 'TPR.G25068' => 'tpr', 'TPR.G31346' => 'tpr', 'TPR.G33334' => 'tpr', 'TWI14G1437' => 'twi', 'TWI23G0325' => 'twi', 'TWI31G0665' => 'twi', 'TWI32G0263' => 'twi', 'TWI34G1314' => 'twi', 'TWI39G0406' => 'twi', 'unitig_0.g1162' => 'ugi', 'unitig_21.g20183' => 'ugi', 'unitig_52.g17542' => 'ugi', 'unitig_61.g26293' => 'ugi', 'unitig_62.g23523' => 'ugi', 'unitig_747.g21762' => 'ugi', 'vmacro06718' => 'vma', 'vmacro09857' => 'vma', 'vmacro13920' => 'vma', 'vmacro14986' => 'vma', 'VMungo0464G0169' => 'vmu', 'VMungo0464G1572' => 'vmu', 'VMungo0647G2027' => 'vmu', 'VMungo1309G1676' => 'vmu', 'Zm00001eb112550' => 'zma', 'Zm00001eb138590' => 'zma', 'Zm00001eb169050' => 'zma', 'Zm00001eb269310' => 'zma', 'Zm00001eb300910' => 'zma', 'Zm00001eb378690' => 'zma', 'Zm00001eb409170' => 'zma' ) $gf_id = 'HOM05D001175' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001175' ) $data_identifier = 'HOM05D001175' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 11, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 10, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 11, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 8, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 7, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 14, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 11, 'ppa' => (int) 11, 'ppe' => (int) 3, 'psa' => (int) 7, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409170' $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